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Dear Olga, You are fitting a model to the data in which the poe.em$data should give you the transformed data that are combinable across studies. By definition, the entries in poe.em$data are not identical to the original data. Debashis -- Debashis Ghosh Associate Professor of Biostatistics University of Michigan 1420 Washington Heights Ann Arbor, MI 48109-2029 email: ghoshd at umich.edu phone: (734) 615-9824 fax: (734) 763-2215 Quoting "Olga K. Kamneva" <kamushkina at="" gmail.com="">: > Hello, all, > > I have some trouble with metaArray package. > I'd like use this package to integrate data from different studies. But it > give unexpected result. > I have data set with 4 time points and 2 repeats for each time. I have an > expression matrix after rma() prepossessing > > >> str(b.rma) > num [1:8641, 1:8] 4.95 3.95 5.48 7.74 5.29 ... > - attr(*, "dimnames")=List of 2 > ..$ : chr [1:8641] "Mm.4517" "Mm.226037" "Mm.338175" "Mm.362588" ... > ..$ : chr [1:8] "X00hr.r..CEL" "X00hr.CEL" "X08hr.r..CEL" "X08hr.CEL" ... >> b.rma[1:5,1:4] > X00hr.r..CEL X00hr.CEL X08hr.r..CEL X08hr.CEL > Mm.4517 4.949947 4.899200 4.814221 4.839363 > Mm.226037 3.946517 4.018580 4.047994 4.000673 > Mm.338175 5.484870 5.458543 5.315563 5.375122 > Mm.362588 7.744338 7.761616 7.414228 7.394226 > Mm.1571 5.294042 5.108926 4.720241 4.825122 >> clb <- c(1, 1, 0, 0, 0, 0, 0, 0) >> b.poe.em<- poe.em(b.rma, cl = clb, threshold=1e-05, every = 3000) > Number of Samples: 8 > Number of Genes: 8641 > This model assumes that the samples are centered and scaled. > 3000 genes fitted > 6000 genes fitted >> b.poe.em$data[1:5,1:4] > X00hr.r..CEL X00hr.CEL X08hr.r..CEL X08hr.CEL > Mm.4517 0.0639460455 0.0096282914 -0.015324771 -0.003167604 > Mm.226037 -0.0221766586 -0.0003496772 0.001001762 -0.002457393 > Mm.338175 -0.0005617508 -0.0057849273 -0.211710552 -0.072901889 > Mm.362588 0.0153744690 0.0215050722 -0.097810670 -0.121062369 > Mm.1571 0.9081874141 0.9081608456 0.015922584 0.247076490 >> > > > I have no idea why data after poe-transformation isn't conformed with > original data. > Looking forward any suggestions! > Olga > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > >

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